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4wma

Crystal structure of mouse Xyloside xylosyltransferase 1 complexed with manganese,acceptor ligand and UDP-Glucose

Method: X-RAY DIFFRACTION Dmax: 68.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Xyloside xylosyltransferase 1

Mus musculus

UniProt Q3U4G3

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 2 其他Polymer 1 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 87–392 Fragment：unp residues 87-392 Coagulation factor IX × 1 （P00740） alpha-D-xylopyranose-(1-3)-beta-D-glucopyranose × 1 MN MANGANESE (II) ION × 1 UPG URIDINE-5'-DIPHOSPHATE-GLUCOSE × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.2 M Li2SO4, 0.1 M Bis-Tris, and 21% PEG3350 Resolution 1.62 Å R-free 0.243

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 4WMA Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4WLG crystal structure of mouse Xyloside xylosyltransferase 1, apo form Deposited 2014-10-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 87–392（306 aa） Fragment：unp residues 87-392
Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；20 mM HEPES, 1.5 M Li2SO4
Resolution 3.00 Å R-free 0.276
4WLG crystal structure of mouse Xyloside xylosyltransferase 1, apo form Deposited 2014-10-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 87–392（306 aa） Fragment：unp residues 87-392
Not recorded SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；20 mM HEPES, 1.5 M Li2SO4
Resolution 3.00 Å R-free 0.276
4WLG crystal structure of mouse Xyloside xylosyltransferase 1, apo form Deposited 2014-10-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 87–392（306 aa） Fragment：unp residues 87-392
Chain B 87–392（306 aa） Fragment：unp residues 87-392
Not recorded SO4 SULFATE ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；20 mM HEPES, 1.5 M Li2SO4
Resolution 3.00 Å R-free 0.276
4WLM Crystal structure of mouse Xyloside xylosyltransferase 1 complexed with manganese Deposited 2014-10-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 87–392（306 aa） Fragment：unp residues 87-392
Not recorded SO4 SULFATE ION × 2 MN MANGANESE (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；20 mM HEPES, 1.5 M Li2SO4
Resolution 3.00 Å R-free 0.287
4WLM Crystal structure of mouse Xyloside xylosyltransferase 1 complexed with manganese Deposited 2014-10-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 87–392（306 aa） Fragment：unp residues 87-392
Not recorded SO4 SULFATE ION × 3 MN MANGANESE (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；20 mM HEPES, 1.5 M Li2SO4
Resolution 3.00 Å R-free 0.287
4WLM Crystal structure of mouse Xyloside xylosyltransferase 1 complexed with manganese Deposited 2014-10-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 87–392（306 aa） Fragment：unp residues 87-392
Chain B 87–392（306 aa） Fragment：unp residues 87-392
Not recorded SO4 SULFATE ION × 5 MN MANGANESE (II) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；20 mM HEPES, 1.5 M Li2SO4
Resolution 3.00 Å R-free 0.287
4WLZ Crystal structure of mouse Xyloside xylosyltransferase 1 complexed with manganese and UDP Deposited 2014-10-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 87–392（306 aa）
Not recorded MN MANGANESE (II) ION × 1 UDP URIDINE-5'-DIPHOSPHATE × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；20 mM HEPES, 1.5 M Li2SO4
Resolution 3.03 Å R-free 0.288
4WLZ Crystal structure of mouse Xyloside xylosyltransferase 1 complexed with manganese and UDP Deposited 2014-10-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 87–392（306 aa）
Not recorded MN MANGANESE (II) ION × 1 UDP URIDINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；20 mM HEPES, 1.5 M Li2SO4
Resolution 3.03 Å R-free 0.288
4WLZ Crystal structure of mouse Xyloside xylosyltransferase 1 complexed with manganese and UDP Deposited 2014-10-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 87–392（306 aa）
Chain B 87–392（306 aa）
Not recorded MN MANGANESE (II) ION × 2 UDP URIDINE-5'-DIPHOSPHATE × 2 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；20 mM HEPES, 1.5 M Li2SO4
Resolution 3.03 Å R-free 0.288
4WM0 Crystal structure of mouse Xyloside xylosyltransferase 1 complexed with acceptor ligand Deposited 2014-10-08 Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 87–392（306 aa） Fragment：unp residues 87-392
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.2 M Li2SO4, 0.1 M Bis-Tris, and 21% PEG3350
Resolution 2.37 Å R-free 0.233
4WMB crystal structure of mouse Xyloside xylosyltransferase 1 complexed with manganese, acceptor ligand and UDP Deposited 2014-10-08 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 87–392（306 aa） Fragment：unp residues 87-392
Not recorded MN MANGANESE (II) ION × 1 UDP URIDINE-5'-DIPHOSPHATE × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.2 M Li2SO4, 0.1 M Bis-Tris, pH 6.5, and 21% PEG3350
Resolution 2.05 Å R-free 0.235
4WMI Crystal structure of mouse Xyloside xylosyltransferase 1 complexed with manganese, product ligand and UDP (Product complex I) Deposited 2014-10-09 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 87–392（306 aa） Fragment：unp residues 87-392
Not recorded MN MANGANESE (II) ION × 1 UDP URIDINE-5'-DIPHOSPHATE × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M Li2SO4, 0.1 M Bis-Tris, pH 6.5, and 21% PEG3350
Resolution 1.87 Å R-free 0.226
4WMK Crystal structure of mouse Xyloside xylosyltransferase 1 complexed with manganese, product ligand and UDP (Product complex II) Deposited 2014-10-09 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 87–392（306 aa） Fragment：unp residues 87-392
Not recorded MN MANGANESE (II) ION × 1 UDP URIDINE-5'-DIPHOSPHATE × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M Li2SO4, 0.1 M Bis-Tris, and 21% PEG3350
Resolution 2.08 Å R-free 0.246
4WN2 Crystal structure of mouse Xyloside xylosyltransferase 1 complexed with manganese, product ligand and UDP (Product complex III) Deposited 2014-10-10 Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 87–392（306 aa） Fragment：unp residues 87-392
Not recorded MN MANGANESE (II) ION × 1 UDP URIDINE-5'-DIPHOSPHATE × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.2 M Li2SO4, 0.1 M Bis-Tris, and 21% PEG3350
Resolution 1.95 Å R-free 0.239
4WNH Crystal structure of mouse Xyloside xylosyltransferase 1 complexed with manganese,acceptor ligand and UDP-Xylose Deposited 2014-10-11 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 87–392（306 aa） Fragment：unp residues 87-392
Not recorded MN MANGANESE (II) ION × 1 UDX URIDINE-5'-DIPHOSPHATE-XYLOPYRANOSE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.2 M Li2SO4, 0.1 M Bis-Tris, pH 6.5, and 21% PEG3350
Resolution 1.95 Å R-free 0.224

9 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name XXLT1_MOUSE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–306； UniProt 87–392

Coagulation factor IX

Homo sapiens

UniProt P00740

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 2 其他Polymer 1 PDB declaration: dimeric（2） Consistent with protein copy count Chain D； UniProt 92–130 Fragment：unp residues 92-130 Xyloside xylosyltransferase 1 × 1 （Q3U4G3） alpha-D-xylopyranose-(1-3)-beta-D-glucopyranose × 1 MN MANGANESE (II) ION × 1 UPG URIDINE-5'-DIPHOSPHATE-GLUCOSE × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.2 M Li2SO4, 0.1 M Bis-Tris, and 21% PEG3350 Resolution 1.62 Å R-free 0.243

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 4WMA Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1CFH STRUCTURE OF THE METAL-FREE GAMMA-CARBOXYGLUTAMIC ACID-RICH MEMBRANE BINDING REGION OF FACTOR IX BY TWO-DIMENSIONAL NMR SPECTROSCOPY Deposited 1995-02-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 47–93（47 aa）
Not recorded FMT FORMIC ACID × 12 SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
1CFI NMR STRUCTURE OF CALCIUM ION-BOUND GAMMA-CARBOXY-GLUTAMIC ACID-RICH DOMAIN OF FACTOR IX Deposited 1995-04-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 47–93（47 aa） Fragment：THE GLA AND AROMATIC AMINO ACID STACK DOMAINS, RESIDUES 1 - 47
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 5.35
Resolution not provided
1EDM EPIDERMAL GROWTH FACTOR-LIKE DOMAIN FROM HUMAN FACTOR IX Deposited 1996-03-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain B 92–130（39 aa） Fragment：EPIDERMAL GROWTH FACTOR-LIKE DOMAIN
Chain C 92–130（39 aa） Fragment：EPIDERMAL GROWTH FACTOR-LIKE DOMAIN
Not recorded CA CALCIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.3；pH 7.3
Resolution 1.50 Å
1IXA THE THREE-DIMENSIONAL STRUCTURE OF THE FIRST EGF-LIKE MODULE OF HUMAN FACTOR IX: COMPARISON WITH EGF AND TGF-A Deposited 1991-11-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 92–130（39 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
1MGX COAGULATION FACTOR, MG(II), NMR, 7 STRUCTURES (BACKBONE ATOMS ONLY) Deposited 1995-06-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 47–93（47 aa） Fragment：THE GLA AND AROMATIC AMINO ACID STACK DOMAINS FROM RESIDUES 1 - 47
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
1NL0 Crystal structure of human factor IX Gla domain in complex of an inhibitory antibody, 10C12 Deposited 2003-01-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 47–91（45 aa） Fragment：Gla domain
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 1 CA CALCIUM ION × 6 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.20 Å R-free 0.270
1NL0 Crystal structure of human factor IX Gla domain in complex of an inhibitory antibody, 10C12 Deposited 2003-01-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain G 47–91（45 aa） Fragment：Gla domain
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 2 CA CALCIUM ION × 12 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.20 Å R-free 0.270
1RFN HUMAN COAGULATION FACTOR IXA IN COMPLEX WITH P-AMINO BENZAMIDINE Deposited 1999-04-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 227–461（235 aa） Fragment：FRAGMENT EGF2-CATALYTIC DOMAIN
Chain B 128–183（56 aa） Fragment：FRAGMENT EGF2-CATALYTIC DOMAIN
Not recorded CA CALCIUM ION × 1 PBZ P-AMINO BENZAMIDINE × 1 TBU TERTIARY-BUTYL ALCOHOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；pH 8.00
Resolution 2.80 Å R-free 0.273
2WPH factor IXa superactive triple mutant Deposited 2009-08-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 133–191（59 aa） Fragment：EGF2 DOMAIN, RESIDUES 133-191
Chain S 227–461（235 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 227-461
Mutation：YES CA CALCIUM ION × 1 1PE PENTAETHYLENE GLYCOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；22 % PEG 3000, 100 MM BIS/TRIS, PH 6.85
Resolution 1.50 Å R-free 0.267
2WPI factor IXa superactive double mutant Deposited 2009-08-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 133–191（59 aa） Fragment：EGF2 DOMAIN, RESIDUES 133-191
Chain S 227–461（235 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 227-461
Mutation：YES CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.1；24 % PEG 6000 100 MM MES PH 7.1
Resolution 1.99 Å R-free 0.252
2WPJ factor IXa superactive triple mutant, NaCl-soaked Deposited 2009-08-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 133–191（59 aa） Fragment：EGF2 DOMAIN, RESIDUES 133-191
Chain S 227–461（235 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 227-461
Mutation：YES CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；22 % PEG 3000 100 MM BIS/TRIS PH 6.85
Resolution 1.60 Å R-free 0.256
2WPK factor IXa superactive triple mutant, ethylene glycol-soaked Deposited 2009-08-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 133–191（59 aa） Fragment：EGF2 DOMAIN, RESIDUES 133-191
Chain S 227–461（235 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 227-461
Mutation：YES CA CALCIUM ION × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；22 % PEG 3000 100 MM BIS/TRIS PH 6.85
Resolution 2.21 Å R-free 0.259
2WPL factor IXa superactive triple mutant, EDTA-soaked Deposited 2009-08-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 133–191（59 aa） Fragment：EGF2 DOMAIN, RESIDUES 133-191
Chain S 227–461（235 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 227-461
Mutation：YES No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；22 % PEG 3000 100 MM BIS/TRIS PH 6.85
Resolution 1.82 Å R-free 0.289
2WPM factor IXa superactive mutant, EGR-CMK inhibited Deposited 2009-08-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 133–191（59 aa） Fragment：EGF2 DOMAIN, RESIDUES 133-191
Chain S 227–461（235 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 227-461
Mutation：YES CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.85；22 % PEG 3000 100 MM BIS/TRIS PH 6.85
Resolution 2.00 Å R-free 0.318
3KCG Crystal structure of the antithrombin-factor IXa-pentasaccharide complex Deposited 2009-10-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain H 227–461（235 aa）
Chain L 131–188（58 aa） Fragment：EGF2
Mutation：S195A CA CALCIUM ION × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；295 K；0.25M Ammonium sulfate, 19.5% PEG 3350, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 1.70 Å R-free 0.230
3LC3 Benzothiophene Inhibitors of Factor IXa Deposited 2010-01-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 227–461（235 aa） Fragment：residues 227-461
Chain B 133–188（56 aa） Fragment：residues 133-188
Not recorded IYX 1-[5-(3,4-dimethoxyphenyl)-1-benzothiophen-2-yl]methanediamine × 2 CA CALCIUM ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.90 Å R-free 0.260
3LC3 Benzothiophene Inhibitors of Factor IXa Deposited 2010-01-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 227–461（235 aa） Fragment：residues 227-461
Chain D 133–188（56 aa） Fragment：residues 133-188
Not recorded IYX 1-[5-(3,4-dimethoxyphenyl)-1-benzothiophen-2-yl]methanediamine × 2 CA CALCIUM ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.90 Å R-free 0.260
3LC5 Selective Benzothiophine Inhibitors of Factor IXa Deposited 2010-01-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 227–461（235 aa） Fragment：residues 227-461
Chain B 133–188（56 aa） Fragment：residues 133-188
Not recorded CA CALCIUM ION × 1 IZX 1-{4-[(R)-phenyl(3-phenyl-1,2,4-oxadiazol-5-yl)methoxy]-1-benzothiophen-2-yl}methanediamine × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.62 Å R-free 0.277
4WM0 Crystal structure of mouse Xyloside xylosyltransferase 1 complexed with acceptor ligand Deposited 2014-10-08 Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 92–130（39 aa） Fragment：unp residues 92-130
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.2 M Li2SO4, 0.1 M Bis-Tris, and 21% PEG3350
Resolution 2.37 Å R-free 0.233
4WMB crystal structure of mouse Xyloside xylosyltransferase 1 complexed with manganese, acceptor ligand and UDP Deposited 2014-10-08 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 92–130（39 aa） Fragment：unp residues 92-130
Not recorded MN MANGANESE (II) ION × 1 UDP URIDINE-5'-DIPHOSPHATE × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.2 M Li2SO4, 0.1 M Bis-Tris, pH 6.5, and 21% PEG3350
Resolution 2.05 Å R-free 0.235
4WMI Crystal structure of mouse Xyloside xylosyltransferase 1 complexed with manganese, product ligand and UDP (Product complex I) Deposited 2014-10-09 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 92–130（39 aa） Fragment：unp residues 92-130
Not recorded MN MANGANESE (II) ION × 1 UDP URIDINE-5'-DIPHOSPHATE × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M Li2SO4, 0.1 M Bis-Tris, pH 6.5, and 21% PEG3350
Resolution 1.87 Å R-free 0.226
4WMK Crystal structure of mouse Xyloside xylosyltransferase 1 complexed with manganese, product ligand and UDP (Product complex II) Deposited 2014-10-09 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 92–130（39 aa） Fragment：unp residues 92-130
Not recorded MN MANGANESE (II) ION × 1 UDP URIDINE-5'-DIPHOSPHATE × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M Li2SO4, 0.1 M Bis-Tris, and 21% PEG3350
Resolution 2.08 Å R-free 0.246
4WN2 Crystal structure of mouse Xyloside xylosyltransferase 1 complexed with manganese, product ligand and UDP (Product complex III) Deposited 2014-10-10 Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 92–130（39 aa） Fragment：unp residues 92-130
Not recorded MN MANGANESE (II) ION × 1 UDP URIDINE-5'-DIPHOSPHATE × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.2 M Li2SO4, 0.1 M Bis-Tris, and 21% PEG3350
Resolution 1.95 Å R-free 0.239
4WNH Crystal structure of mouse Xyloside xylosyltransferase 1 complexed with manganese,acceptor ligand and UDP-Xylose Deposited 2014-10-11 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 92–130（39 aa） Fragment：unp residues 92-130
Not recorded MN MANGANESE (II) ION × 1 UDX URIDINE-5'-DIPHOSPHATE-XYLOPYRANOSE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.2 M Li2SO4, 0.1 M Bis-Tris, pH 6.5, and 21% PEG3350
Resolution 1.95 Å R-free 0.224
4YZU Rapid development of two Factor IXa inhibitors from Hit to Lead Deposited 2015-03-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 227–461（235 aa） Fragment：Peptidase S1 domain (UNP residue 227-461)
Chain B 131–191（61 aa） Fragment：EGF-like 2 domain (UNP residues 131-191)
Mutation：R150A 4K6 N-[2-(5,6-dimethyl-1H-benzimidazol-2-yl)ethyl]-4-(4H-1,2,4-triazol-4-yl)benzamide × 1 NA SODIUM ION × 1 NHE 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9.5；295 K；0.05 M Tris, pH 7.2, 1.2 M ammonium sulfate, 2.0 M sodium chloride
Resolution 1.41 Å R-free 0.161
4Z0K Rapid development of two Factor IXa inhibitors from Hit to Lead Deposited 2015-03-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 227–461（235 aa） Fragment：Peptidase S1 domain (UNP residue 227-461)
Chain B 131–191（61 aa） Fragment：EGF-like 2 domain (UNP residues 131-191)
Not recorded 4LN N-[(2R)-10-hydroxy-2,7-dimethyl-1,2,3,4-tetrahydropyrido[1,2-b]indazol-2-yl]-4-(4H-1,2,4-triazol-4-yl)benzamide × 1 NA SODIUM ION × 1 NHE 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；295 K；50 mM Tris, pH 7.2, 1.2 M ammonium sulfate, 2.0 M sodium chloride
Resolution 1.41 Å R-free 0.165
4ZAE Development of a novel class of potent and selective FIXa inhibitors Deposited 2015-04-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 227–461（235 aa） Fragment：Peptidase S1 domain (UNP residues 227-461)
Chain B 131–191（61 aa） Fragment：EG-like 2 domain (UNP residues 131-191)
Mutation：R150A 4M1 2,6-dichloro-N-[(2R)-2-(5,6-dimethyl-1H-benzimidazol-2-yl)-2-phenylethyl]-4-(4H-1,2,4-triazol-4-yl)benzamide × 1 NA SODIUM ION × 1 NHE 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；295 K；50 mM CHES, pH 9.0, 1.3 M tri-sodium citrate and 3 mM compound (cross seeded with crystals grown from 50 mM Tris, pH 7.2, 1.45 M ammonium sulfate, 2.0 M sodium chloride and 3 mM compound)
Resolution 1.86 Å R-free 0.174
5EGM Development of a novel tricyclic class of potent and selective FIXa inhibitors Deposited 2015-10-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 227–461（235 aa）
Chain B 131–191（61 aa） Fragment：UNP residues 131-191
Mutation：A150R NA SODIUM ION × 1 NHE 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID × 1 5NY 2-chloranyl-~{N}-[(7~{S})-2-methyl-7-phenyl-10-(1~{H}-1,2,3,4-tetrazol-5-yl)-8,9-dihydro-6~{H}-pyrido[1,2-a]indol-7-yl]-4-(1,2,4-triazol-4-yl)benzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；295 K；50 MM CHES, PH 9.0, 1.3 M TRI-SODIUM REMARK 280 CITRATE AND 3 MM COMPOUND (CROSS SEEDED WITH CRYSTALS GROWN FROM REMARK 280 50 MM TRIS, PH 7.2, 1.45 M AMMONIUM SULFATE, 2.0 M SODIUM REMARK 280 CHLORIDE AND 3 MM COMPOUND)
Resolution 1.84 Å R-free 0.171
5F84 Crystal structure of Drosophila Poglut1 (Rumi) complexed with its glycoprotein product (glucosylated EGF repeat) and UDP Deposited 2015-12-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 92–130（39 aa） Fragment：UNP residues 92-130
Not recorded UDP URIDINE-5'-DIPHOSPHATE × 1 SO4 SULFATE ION × 5 BGC beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；1.62M ammonium sulfate
Resolution 2.50 Å R-free 0.239
5F85 Crystal structure of Drosophila Poglut1 (Rumi) complexed with its substrate protein (EGF repeat) and UDP Deposited 2015-12-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 92–130（39 aa） Fragment：UNP residues 92-130
Not recorded UDP URIDINE-5'-DIPHOSPHATE × 1 GOL GLYCEROL × 1 SO4 SULFATE ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；1.62M ammonium sulfate
Resolution 2.15 Å R-free 0.243
5F86 Crystal structure of Drosophila Poglut1 (Rumi) complexed with its substrate protein (EGF repeat) Deposited 2015-12-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 92–130（39 aa） Fragment：UNP residues 92-130
Not recorded GOL GLYCEROL × 1 SO4 SULFATE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；1.62M ammonium sulfate
Resolution 1.90 Å R-free 0.221
5JB8 Crystal structure of factor IXa variant K98T in complex with EGR-chloromethylketone Deposited 2016-04-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain E 134–191（58 aa）
Chain S 227–461（235 aa）
Mutation：K98T CA CALCIUM ION × 1 0GJ L-alpha-glutamyl-N-{(1S)-4-{[amino(iminio)methyl]amino}-1-[(1S)-2-chloro-1-hydroxyethyl]butyl}glycinamide × 1 DMS DIMETHYL SULFOXIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；6 mg/mL protein-inhibitor complex, 0.1M MES pH 6.5, 18-20% PEG6000
Resolution 1.45 Å R-free 0.185
5JB9 Crystal structure of factor IXa K98T variant in complex with PPACK Deposited 2016-04-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain E 134–191（58 aa）
Chain S 227–461（235 aa）
Mutation：K98T 0G6 D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide × 1 CA CALCIUM ION × 1 DMS DIMETHYL SULFOXIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；6 mg/mL protein/inhibitor complex 0.1 M MES pH 6.5 18% PEG6000
Resolution 1.30 Å R-free 0.176
5JBA Crystal structure of factor IXa variant V16I K98T Y177T I212V in complex with PPACK Deposited 2016-04-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain E 134–191（58 aa）
Chain S 227–461（235 aa）
Mutation：V16I K98T Y177T I212V CA CALCIUM ION × 1 0G6 D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide × 1 DMS DIMETHYL SULFOXIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；6 mg/mL protein-inhibitor complex, 0.1M MES pH 6.5, 18% PEG6000
Resolution 1.40 Å R-free 0.179
5JBB Crystal structure of factor IXa variant V16I K98T Y177T I213V in complex with EGR-chloromethylketone Deposited 2016-04-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain E 134–191（58 aa）
Chain S 227–461（235 aa）
Mutation：V16I K98T Y177T I213V CA CALCIUM ION × 1 0GJ L-alpha-glutamyl-N-{(1S)-4-{[amino(iminio)methyl]amino}-1-[(1S)-2-chloro-1-hydroxyethyl]butyl}glycinamide × 1 DMS DIMETHYL SULFOXIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；6 mg/mL protein-inhibitor complex, 0.1M MES pH 6.5, 20% PEG6000
Resolution 1.56 Å R-free 0.190
5JBC Crystal structure of factor IXa variant V16I K98T Y177T I213V in complex with PPACK Deposited 2016-04-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain E 134–191（58 aa）
Chain S 227–461（235 aa）
Mutation：V16I K98T Y177T I213V CA CALCIUM ION × 1 0G6 D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；6 mg/mL protein-inhibitor complex, 0.1M MES pH 6.5, 20% PEG6000
Resolution 1.90 Å R-free 0.213
5TNO Discovery of novel aminobenzisoxazole derivatives as orally available factor IXa inhibitors Deposited 2016-10-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 227–461（235 aa） Fragment：UNP residues 227-461
Chain B 131–191（61 aa） Fragment：UNP residues 131-191
Not recorded UNL UNKNOWN LIGAND × 1 NA SODIUM ION × 1 NHE 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；295 K；50 MM CHES, PH 9.0, 1.3 M TRI-SODIUM CITRATE AND 3 MM COMPOUND (CROSS SEEDED WITH CRYSTALS GROWN FROM REMARK 280 50 MM TRIS, PH 7.2, 1.45 M AMMONIUM SULFATE, 2.0 M SODIUM REMARK 280 CHLORIDE AND 3 MM COMPOUND)
Resolution 1.54 Å R-free 0.158
5TNT Discovery of novel aminobenzisoxazole derivatives as orally available factor IXa inhibitors Deposited 2016-10-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 227–461（235 aa） Fragment：UNP residues 227-461
Chain B 131–191（61 aa） Fragment：UNP residues 131-191
Mutation：R150A 7GQ N-[(1S,4S,7R)-2-(3-amino-4-chloro[1,2]oxazolo[5,4-c]pyridin-7-yl)-2-azabicyclo[2.2.1]heptan-7-yl]-2-chloro-4-(3-methyl-1H-1,2,4-triazol-1-yl)benzamide × 1 NA SODIUM ION × 1 NHE 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；295 K；50 MM CHES, PH 9.0, 1.3 M TRI-SODIUM CITRATE AND 3 MM COMPOUND (CROSS SEEDED WITH CRYSTALS GROWN FROM REMARK 280 50 MM TRIS, PH 7.2, 1.45 M AMMONIUM SULFATE, 2.0 M SODIUM CHLORIDE AND 3 MM COMPOUND)
Resolution 1.40 Å R-free 0.161
5VYG Crystal structure of hFA9 EGF repeat with O-glucose trisaccharide Deposited 2017-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain B 92–130（39 aa）
Not recorded CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Tris pH 8.5, 15% Glycerol, 1.6 M (NH4)2SO4, 5% 2,2,2-Trifluoroethanol
Resolution 2.20 Å R-free 0.259
5VYG Crystal structure of hFA9 EGF repeat with O-glucose trisaccharide Deposited 2017-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 92–130（39 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Tris pH 8.5, 15% Glycerol, 1.6 M (NH4)2SO4, 5% 2,2,2-Trifluoroethanol
Resolution 2.20 Å R-free 0.259
5VYG Crystal structure of hFA9 EGF repeat with O-glucose trisaccharide Deposited 2017-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain C 92–130（39 aa）
Not recorded CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Tris pH 8.5, 15% Glycerol, 1.6 M (NH4)2SO4, 5% 2,2,2-Trifluoroethanol
Resolution 2.20 Å R-free 0.259
6MV4 CRYSTAL STRUCTURE OF HUMAN COAGULATION FACTOR IXa Deposited 2018-10-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric
Chain H 227–461（235 aa）
Chain L 133–185（53 aa）
Not recorded SO4 SULFATE ION × 24 EDO 1,2-ETHANEDIOL × 8 FMT FORMIC ACID × 4 PBZ P-AMINO BENZAMIDINE × 4 CA CALCIUM ION × 4 NA SODIUM ION × 4 CL CHLORIDE ION × 12 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；15% PEG4000, 1 M NaCl, 0.2 M Ammonium Sulfate, 5 mM Calcium Chloride
Resolution 1.37 Å R-free 0.210
6RFK Crystal structure of EGRCK-inhibited Gla-domainless fIXa (K148Q, R150Q variant) Deposited 2019-04-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 130–191（62 aa）
Chain S 227–461（235 aa）
Not recorded B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 CA CALCIUM ION × 1 GOL GLYCEROL × 10 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；297 K；0.1M BIS-TRIS propane pH 8.5, 24% PEG 3350, 0.275M Na Malonate
Resolution 1.60 Å R-free 0.163
6X5J Discovery of Hydroxy Pyrimidine Factor IXa Inhibitors Deposited 2020-05-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 227–461（235 aa）
Chain B 131–191（61 aa）
Not recorded GOL GLYCEROL × 2 6NH 2-(4-HYDROXY-5-PHENYL-1H-PYRAZOL-3-YL)-1H-BENZOIMIDAZOLE-5-CARBOXAMIDINE × 1 NA SODIUM ION × 1 CIT CITRIC ACID × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；0.1M CITRIC ACID, 20% PEG 6000
Resolution 2.51 Å R-free 0.225
6X5L Discovery of Hydroxy Pyrimidine Factor IXa Inhibitors Deposited 2020-05-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 227–460（234 aa）
Chain B 131–191（61 aa）
Not recorded UQG 4-{[5-hydroxy-6-(4-methylphenyl)pyrimidin-4-yl]amino}benzene-1-carboximidamide × 1 NA SODIUM ION × 1 CIT CITRIC ACID × 4 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；0.1M CITRIC ACID, 20% PEG 6000
Resolution 2.25 Å R-free 0.233
6X5P Discovery of Hydroxy Pyrimidine Factor IXa Inhibitors Deposited 2020-05-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 227–461（235 aa）
Chain B 131–191（61 aa）
Mutation：A138R UQD 3-chloro-4-{[5-hydroxy-6-(4-methylphenyl)pyrimidin-4-yl]amino}benzene-1-carboximidamide × 1 CIT CITRIC ACID × 4 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；0.1 M CITRIC ACID, 20% PEG 6000
Resolution 2.00 Å R-free 0.239
7AHV Anti-FIXa Fab of mim8 in complex with human FIXa Deposited 2020-09-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain H 227–461（235 aa）
Chain L 131–188（58 aa）
Not recorded SO4 SULFATE ION × 17 0GJ L-alpha-glutamyl-N-{(1S)-4-{[amino(iminio)methyl]amino}-1-[(1S)-2-chloro-1-hydroxyethyl]butyl}glycinamide × 1 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；2 M ammonium sulphate, 0.1 M Hepes, pH 7.5
Resolution 3.11 Å R-free 0.283
8EPC Crystal structure of human coagulation factor IXa (S195A), apo-form Deposited 2022-10-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 130–190（61 aa） Fragment：furin cleavage site (RRKR) inserted
Chain B 227–461（235 aa）
Mutation：S195A CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；40% Glycerol Ethoxylate
Resolution 2.51 Å R-free 0.281
8EPH Crystal structure of human coagulation factor IXa (S195A), apo-form, DES-GLA Deposited 2022-10-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 93–190（98 aa） Fragment：furin cleavage site (RRKR) inserted
Chain B 227–461（235 aa）
Mutation：S195A FUC alpha-L-fucopyranose × 1 CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.1 M Na Citrate pH 5.0; 30% Jeffamine ED-2001 pH 7.0
Resolution 1.88 Å R-free 0.211
8EPH Crystal structure of human coagulation factor IXa (S195A), apo-form, DES-GLA Deposited 2022-10-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 93–190（98 aa） Fragment：furin cleavage site (RRKR) inserted
Chain D 227–461（235 aa）
Mutation：S195A FUC alpha-L-fucopyranose × 1 CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.1 M Na Citrate pH 5.0; 30% Jeffamine ED-2001 pH 7.0
Resolution 1.88 Å R-free 0.211
8EPK Complex of anticoagulant RNA aptamer and human coagulation factor IXa (S195A) Deposited 2022-10-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Homooligomer；Protein × 2 PDB declaration: trimeric
Chain A 130–190（61 aa） Fragment：furin cleavage site (RRKR) inserted
Chain B 227–461（235 aa）
Mutation：S195A CA CALCIUM ION × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；60 mM Na Citrate pH 5.0; 4% Tacsimate pH 7.0; 23% PEG 8000
Resolution 2.65 Å R-free 0.261
8EPK Complex of anticoagulant RNA aptamer and human coagulation factor IXa (S195A) Deposited 2022-10-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Homooligomer；Protein × 2 PDB declaration: trimeric
Chain C 130–190（61 aa） Fragment：furin cleavage site (RRKR) inserted
Chain D 227–461（235 aa）
Mutation：S195A CA CALCIUM ION × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；60 mM Na Citrate pH 5.0; 4% Tacsimate pH 7.0; 23% PEG 8000
Resolution 2.65 Å R-free 0.261
8OL9 Anti-FIXa Fab in complex with human des-(Gla-EGF1) FIXa Deposited 2023-03-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain H 227–461（235 aa）
Chain L 131–188（58 aa）
Not recorded SO4 SULFATE ION × 2 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 CA CALCIUM ION × 1 0GJ L-alpha-glutamyl-N-{(1S)-4-{[amino(iminio)methyl]amino}-1-[(1S)-2-chloro-1-hydroxyethyl]butyl}glycinamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；291 K；0.5 M ammonium sulphate, 0.1 M sodium citrate, pH 5.6, !.0 M lithium sulphate
Resolution 2.60 Å R-free 0.323
9BVK Vitamin K-dependent gamma-carboxylase with factor IX propeptide and glutamate-rich region and with vitamin K hydroquinone Deposited 2024-05-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain P 29–92（64 aa） Fragment：residues 29-92
Not recorded A1AVC vitamin K1 hydroquinone × 1 6PL (4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
9BVR Vitamin K-dependent gamma-carboxylase with factor IX propeptide and partially carboxylated glutamate-rich region and with vitamin K hydroquinone and calcium Deposited 2024-05-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain P 29–92（64 aa） Fragment：residues 29-92
Not recorded A1AVC vitamin K1 hydroquinone × 1 6PL (4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
9L21 cryo-EM structure of Vitamin K-dependent gamma-carboxylase complexed with factor IX Deposited 2024-12-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 29–56（28 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 A1AVC vitamin K1 hydroquinone × 1 BCT BICARBONATE ION × 1 CO2 CARBON DIOXIDE × 1 CLR CHOLESTEROL × 1 PEE 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine × 3 Y01 CHOLESTEROL HEMISUCCINATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.62 Å
9L25 cryo-EM structure of Vitamin K-dependent gamma-carboxylase complexed with factor IX(Gla) Deposited 2024-12-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 29–56（28 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 A1AVC vitamin K1 hydroquinone × 1 CLR CHOLESTEROL × 1 PEE 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine × 3 Y01 CHOLESTEROL HEMISUCCINATE × 1 CO2 CARBON DIOXIDE × 1 BCT BICARBONATE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.41 Å
9L6Q Vitamin K-dependent gamma-carboxylase in complex with Coagulation factor IX and vitamin K Deposited 2024-12-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–461（461 aa）
Not recorded 6PL (4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE × 2 CLR CHOLESTEROL × 1 1L3 Menaquinone-4 × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.78 Å
9L6R double-mutant (K217A & K218A) Vitamin K-dependent gamma-carboxylase in complex with Coagulation factor IX and vitamin K Deposited 2024-12-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–461（461 aa）
Not recorded A1EMC 2-methyl-3-[(2~{E},6~{E},10~{E})-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraenyl]naphthalene-1,4-diol × 1 6PL (4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE × 2 CLR CHOLESTEROL × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.59 Å
9WF3 Cryo-EM structure of GGCX-FIX complex Deposited 2025-08-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 29–56（28 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 2 MX7 (2R)-3-(phosphonooxy)propane-1,2-diyl (9Z,9'Z)bis-octadec-9-enoate × 1 CLR CHOLESTEROL × 1 A1AT1 (1aR,7aS)-1a-methyl-7a-[(2E,6E,10E)-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraen-1-yl]-1a,7a-dihydronaphtho[2,3-b]oxirene-2,7-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.65 Å
9WFN Cryo-EM structure of GGCX-proP2 Deposited 2025-08-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 29–44（16 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 2 MX7 (2R)-3-(phosphonooxy)propane-1,2-diyl (9Z,9'Z)bis-octadec-9-enoate × 1 CLR CHOLESTEROL × 1 A1AT1 (1aR,7aS)-1a-methyl-7a-[(2E,6E,10E)-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraen-1-yl]-1a,7a-dihydronaphtho[2,3-b]oxirene-2,7-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.94 Å

55 other PDB entries and 61 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name FA9_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain D； PDBConstruct 4–42； UniProt 92–130

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 4wma

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4wma
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4wma
Deposition date deposition_date2014-10-08
Structure title titleCrystal structure of mouse Xyloside xylosyltransferase 1 complexed with manganese,acceptor ligand and UDP-Glucose
Keywords keywordsglycosyltransferase, transferase-protein binding complex; transferase/protein binding
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier20.81 Å
Radius of gyration Rg (electron density) rg_electron19.78 Å
Forward intensity I(0) i026717700.00
Molecular weight molecular_weight39366.0 kDa
Excluded volume excluded_volume49069 ų
Envelope volume envelope_volume56946 ų
Hydration-shell volume shell_volume23341 ų
Envelope diameter envelope_diameter73.1 Å
Shell Rg shell_rg26.99 Å
Envelope Rg envelope_rg20.24 Å
Shape Rg shape_rg19.81 Å
Total Rg total_rg20.63 Å
Total atoms total_atoms2765
Residues n_residues334
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax68.8 Å
Rg (real space) rg_real20.70 Å
Rg uncertainty (real space) rg_real_error0.45 Å
I(0) (real space) i0_real2.6720e+07
I(0) uncertainty (real space) i0_real_error3.7210e+05
Rg (reciprocal space) rg_reciprocal20.72 Å
I(0) (reciprocal space) i0_reciprocal26720000.0000
Solution quality estimate total_estimate0.7971
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary25.9 Å
Skewness Skewness skewness0.241
Kurtosis Kurtosis kurtosis-0.261
Angular range angular_range— – 0.3800 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha6027000.0000
Real-space data points n_real_points70
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.787; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

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7. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd4wmad_
Class classg — Small proteins
Fold Fold foldg.3 — Knottins (small inhibitors, toxins, lectins)
Superfamily Superfamily superfamilyg.3.11 — EGF/Laminin
Family Family familyg.3.11.1 — EGF-type module
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8. Citations (1)

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9. Files and Curves (10)